Test-drive the GATK tools and Best Practices pipelines on Terra


Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.

SAMtools bam_sort_core truncated file.

fizwitfizwit Fred Hutch Cancer Research CenterMember

using samtools-1.3.1
getting error about bgzf reads

samtools sort -n -m 4G --threads 4 -o out.bam xxx_hg19_Illumina_gdc_realn.bam

[E::inflate_block] inflate failed: invalid distance too far back
[E::bgzf_read_block] inflate_block error -1
[E::bgzf_read] bgzf_read_block error -1 after 234 of 439 bytes
[bam_sort_core] truncated file. Aborting.

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